The simplified molecular-input line-entry system (SMILES) is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. It describes the connectivity between the atoms, but not the 3D coordinates of your molecules.

See chapter 9 in this documentation (pdf): https://media.readthedocs.org/pdf/open-babel/latest/open-babel.pdf

on how to convert your molecule to 3D in openBabel.

Thank you very much!

You can get molecular description and coordinates with the program AceDRG. Atomic distances and angles are derived from similar bonds in small molecule crystal structures.

You may use OpenEye toolkits to do this. It's will be a few-string code:

from openeye import oechem

a=oechem.oemolistream('Input_SMILES_file')

b=oechem.oemolostream('output_file.pdb')

for mol in a.GetOEGraphMols():

oechem.OEWriteMolecule(b, mol)

Hi Yang

To make a long story short, and keeping to the openbabel tools:

0) have your smi file cleaned of unnecessary info. Just smiles molecule_name

c1ccccc1 benzene

1) Convert your smiles into 3D with program obgen, i.e. for a file example .smi

obgen example.smi > example.sdf

2) Further convert the resulting sdf into any other file format with babel

babel example.sdf example.pdb

Best,

Sandro

To make a long story even shorter:

`PROMPT> obabel -:"" --gen3d -o -O`

Even using Openbabel

http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html

Try on https://cactus.nci.nih.gov/translate/

http://pasilla.health.unm.edu/tomcat/biocomp/convert

This link may help:

https://www.youtube.com/watch?v=uobRSy5p1ZU&t=182s